Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility.

Genome Research
Qiao Rui XingYuin-Han Loh

Abstract

Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human cells of various lineage origins (BJ, K562, JK1, and Jurkat), and 480 primary cord blood cells undergoing erythroblast differentiation. With the joint profiles, we configured the transcriptional and chromatin accessibility landscapes of discrete cell states, uncovered linked sets of cis-regulatory elements and target genes unique to each state, and constructed interactome and transcription factor (TF)-centered upstream regulatory networks for various cell states.

Associated Datasets

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Citations

Feb 20, 2021·Stem Cells International·Zi Hao ZhengYuin-Han Loh
Mar 18, 2021·Annual Review of Plant Biology·Carolin SeyfferthBert De Rybel
Aug 15, 2021·Current Opinion in Plant Biology·Alexandre P Marand, Robert J Schmitz
Sep 30, 2021·Nature Communications·Pradeep GautamYuin-Han Loh
Oct 3, 2021·Genome Research·Andrew C Adey
Nov 3, 2021·Nature Methods·Tim StuartRahul Satija

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